General Sinclair pleaded guilty to maltreatment of his accuser, a military intelligence officer, admitting that his behavior could have caused her "mental harm or suffering" during their affair that spanned two war zones

FORT BRAGG, N.C., March 17 (Reuters) - A U.S. Army general at the center of a rare court-martial of a top military leader was cleared of sexual assault charges on Monday, but admitted mistreating a junior officer during their illicit sexual relationship.

Brigadier General Jeffrey Sinclair also pleaded guilty to misusing his government credit card in connection with the affair and referring to other female officers with derogatory names as part of an agreement with the government that dismissed the most serious allegations against him.

The 27-year Army veteran said he knew the female Army captain with whom he had a three-year extramarital affair was enamored by his rank, and he led her on despite knowing he would never divorce his wife.

When he grew fearful that his subordinate would expose what he said was a consensual relationship, he flirted with other women and was cold to her in hopes she would break off the secret liaison that spanned two war zones, Sinclair told a judge.

"I failed her as a leader and as a mentor and caused her harm to her emotional state," the one-star general said.

Though the deal absolves Sinclair of charges that he forced the captain 17 years his junior to perform oral sex, engaged in "open and notorious sexual acts" with her and threatened to harm her if she exposed the affair, his decorated military career is almost certainly over.

Sinclair's attorneys will argue during the sentencing phase on Monday that he should avoid jail time and be allowed to retire at a reduced rank in keeping with how officers in similar cases have been treated.

The lawyers say Sinclair's case is one of the few courts-martial of a general in nearly 60 years and was fueled by political concerns as the U.S. military grapples with how to handle rising sexual assault in its ranks.

"Clearly what General Sinclair did was wrong, but it certainly had the appearance that he was being the scapegoat for the bigger sexual assault problem that the military’s going through," said Morris Davis, a retired Air Force colonel and former chief prosecutor for terrorism trials at Guantanamo Bay, Cuba, who is not involved in the case.

ACCUSER STANDS BY ALLEGATIONS

An attorney for the captain who gave tearful testimony about her volatile relationship with Sinclair said she maintained that he sexually assaulted her and sabotaged her career by keeping her under his command.

"She was literally trapped and bullied by one of the highest ranking officers in the United States Army," said retired Rear Admiral Jamie Barnett, a partner in the Washington, D.C., law firm of Venable LLP.

"She accepts the plea bargain as a deal that allows her to get on with her life and career, but she stands by every word of her testimony about his sexual assault," Barnett added.

The identity of the captain, a military intelligence officer, is being withheld by Reuters due to the nature of the charges.

Sinclair, a 51-year-old married father of two, has remained on active duty at the sprawling base at Fort Bragg after being stripped of command in southern Afghanistan in May 2012 as a result of the criminal allegations.

His trial was already under way this month when a judge ruled that politics appeared to have improperly influenced the Army's decision to reject an earlier offer by Sinclair to plead guilty if the charges of coercive sex acts were dropped.

The former lead prosecutor in the case resigned after military leaders refused to dismiss the sex charges despite concerns about the key accuser's credibility, with Army officials saying they did not doubt her underlying allegations. The court-martial was delayed before Sinclair's defense team got to cross-examine the woman.

The judge last week allowed Sinclair to renew his plea offer. The agreement reached over the weekend called for the government to drop the sexual assault charges involving the captain, as well as two additional charges that could have required Sinclair to register as a sex offender.

In addition to pleading guilty to maltreating his accuser, Sinclair admitted to calling a female major "a red-headed troll" but told the judge he was joking when he said "I'm a general, I'll say whatever the fuck I want."

The general also faces punishment after pleading guilty this month to having an adulterous affair, asking junior female officers for nude photos and possessing pornography on his laptop while deployed in Afghanistan.

He could have been sent to prison for life if he had been convicted of the sexual assault charges, but now faces a maximum confinement of 25-1/2 years.